Revert of Have apply_patch.py/checkout.py stage git patches instead of committing them (https://codereview.chromium.org/273543002/)

Reason for revert:
Borked all the tryjobs due to missing --base_ref, needed to land with https://codereview.chromium.org/273543002/

Original issue's description:
> Have apply_patch.py/checkout.py stage git patches instead of committing them
> 
> For a bot_update Git world, we don't really want to commit patches.  Instead
> we just want to leave them unstaged.
> 
> BUG=370503
> TEST=ran locally with and without flag
> 
> Committed: http://src.chromium.org/viewvc/chrome?view=rev&revision=269468

TBR=maruel@chromium.org,agable@chromium.org,hinoka@google.com,iannucci@chromium.org
NOTREECHECKS=true
NOTRY=true
BUG=370503

Review URL: https://codereview.chromium.org/271283003

git-svn-id: svn://svn.chromium.org/chrome/trunk/tools/depot_tools@269482 0039d316-1c4b-4281-b951-d872f2087c98